pappso::MsRunReaderScanNumberMultiMap Class Reference

provides a multimap to find quickly spectrum index from scan number More...

#include <msrunreader.h>

Inheritance diagram for pappso::MsRunReaderScanNumberMultiMap:

Public Member Functions
	MsRunReaderScanNumberMultiMap ()
virtual	~MsRunReaderScanNumberMultiMap ()
virtual void	setQualifiedMassSpectrum (const QualifiedMassSpectrum &spectrum) override
virtual bool	needPeakList () const override
	tells if we need the peak list (if we want the binary data) for each spectrum More...
std::size_t	getSpectrumIndexFromScanNumber (std::size_t scan_number) const
Public Member Functions inherited from pappso::SpectrumCollectionHandlerInterface
virtual bool	needMsLevelPeakList (unsigned int ms_level) const final
	tells if we need the peak list (if we want the binary data) for each spectrum, given an MS level More...
virtual void	setNeedMsLevelPeakList (unsigned int ms_level, bool want_peak_list) final
	tells if we need the peak list given More...
virtual bool	shouldStop ()
virtual void	loadingEnded ()
virtual void	spectrumListHasSize (std::size_t size)
virtual void	setReadAhead (bool is_read_ahead) final
	use threads to read a spectrum by batch of batch_size More...
virtual bool	isReadAhead () const
	tells if we want to read ahead spectrum More...

Private Attributes
std::multimap< std::size_t, std::size_t >	m_mmap_scan2index

Detailed Description

provides a multimap to find quickly spectrum index from scan number

Definition at line 151 of file msrunreader.h.

Constructor & Destructor Documentation

MsRunReaderScanNumberMultiMap()

pappso::MsRunReaderScanNumberMultiMap::MsRunReaderScanNumberMultiMap

(

)

Definition at line 150 of file msrunreader.cpp.

{
  qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()";

~MsRunReaderScanNumberMultiMap()

pappso::MsRunReaderScanNumberMultiMap::~MsRunReaderScanNumberMultiMap ( )

virtual

Definition at line 154 of file msrunreader.cpp.

{
  qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()";

Member Function Documentation

getSpectrumIndexFromScanNumber()

std::size_t pappso::MsRunReaderScanNumberMultiMap::getSpectrumIndexFromScanNumber

(

std::size_t

scan_number

)

const

Definition at line 188 of file msrunreader.cpp.

{
 
  qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
           << " " << m_mmap_scan2index.size();
  auto it = m_mmap_scan2index.find(scan_number);
  if(it == m_mmap_scan2index.end())
    {
      throw ExceptionNotFound(
        QObject::tr("scan number %1 not found").arg(scan_number));
    }
  std::size_t index = it->second;
  it++;
  if((it != m_mmap_scan2index.end()) && (it->first == scan_number))
    {
      throw PappsoException(
        QObject::tr("scan number %1 found multiple times").arg(scan_number));
    }
  return index;

References m_mmap_scan2index.

Referenced by pappso::MsRunReader::scanNumber2SpectrumIndex().

needPeakList()

bool pappso::MsRunReaderScanNumberMultiMap::needPeakList ( ) const

overridevirtual

tells if we need the peak list (if we want the binary data) for each spectrum

Implements pappso::SpectrumCollectionHandlerInterface.

Definition at line 159 of file msrunreader.cpp.

{
  return false;

setQualifiedMassSpectrum()

void pappso::MsRunReaderScanNumberMultiMap::setQualifiedMassSpectrum ( const QualifiedMassSpectrum &  spectrum )

overridevirtual

Implements pappso::SpectrumCollectionHandlerInterface.

Definition at line 165 of file msrunreader.cpp.

{
  qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
           << " " << qspectrum.getMassSpectrumId().getNativeId();
  QStringList native_id_list =
    qspectrum.getMassSpectrumId().getNativeId().split("=");
  if(native_id_list.size() < 2)
    {
      return;
    }
  else
    {
      std::size_t scan_number = native_id_list.back().toULong();
      m_mmap_scan2index.insert(std::pair<std::size_t, std::size_t>(
        scan_number, qspectrum.getMassSpectrumId().getSpectrumIndex()));
      qDebug() << __FILE__ << "@" << __LINE__ << __FUNCTION__ << "()"
               << " " << scan_number << "=>"
               << qspectrum.getMassSpectrumId().getSpectrumIndex();
    }

References pappso::QualifiedMassSpectrum::getMassSpectrumId(), pappso::MassSpectrumId::getNativeId(), pappso::MassSpectrumId::getSpectrumIndex(), and m_mmap_scan2index.

Member Data Documentation

m_mmap_scan2index

std::multimap<std::size_t, std::size_t> pappso::MsRunReaderScanNumberMultiMap::m_mmap_scan2index

private

Definition at line 154 of file msrunreader.h.

Referenced by getSpectrumIndexFromScanNumber(), and setQualifiedMassSpectrum().

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The documentation for this class was generated from the following files:

• pappsomspp/msrun/msrunreader.h
• pappsomspp/msrun/msrunreader.cpp